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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ), 'gf_id' => 'HOM05D001181', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001181' ), 'data_identifier' => 'HOM05D001181', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001181', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04240' => 'bna', 'A03p41240' => 'bna', 'A03p62730' => 'bna', 'A07p30310' => 'bna', 'A08p17010' => 'bna', 'A08p30760' => 'bna', 'Aa31LG2G16670' => 'aar', 'Aa31LG4G8370' => 'aar', 'Aa31LG7G2570' => 'aar', 'Aa31LG8G6210' => 'aar', 'Aa31LG8G6230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1380' => 'aag', 'Actinidia00416' => 'ach', 'Actinidia01077' => 'ach', 'Actinidia14042' => 'ach', 'Actinidia17884' => 'ach', 'Actinidia21859' => 'ach', 'Actinidia22321' => 'ach', 'Actinidia27969' => 'ach', 'Actinidia33817' => 'ach', 'Ah.01g018190' => 'amhyb', 'Ah.05g178750' => 'amhyb', 'Ah.14g085760' => 'amhyb', 'Ah.15g091480' => 'amhyb', 'AL1G30090' => 'aly', 'AL2G31860' => 'aly', 'AL3G32880' => 'aly', 'AL3G47060' => 'aly', 'AL7G17110' => 'aly', 'Aqoxy5G01152' => 'aox', 'Aqoxy6G02411' => 'aox', 'Aqoxy7G03179' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ZF6Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.158GZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2GTZ8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3MHK8M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45MQKA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.53YFBS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I0SN9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASS065' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AT90LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AV6GAN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DDAS79' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MRKD4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P6RS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZVW0EZ' => 'arhy', 'AT1G17745' => 'ath', 'AT1G72190' => 'ath', 'AT3G19480' => 'ath', 'AT4G34200' => 'ath', 'ATR0580G020' => 'atr', 'ATR0724G083' => 'atr', 'ATR1136G036' => 'atr', 'ATR1136G151' => 'atr', 'Atru.chr1.2774' => 'acertr', 'Atru.chr13.2345' => 'acertr', 'Atru.chr13.755' => 'acertr', 'Atru.chr5.2583' => 'acertr', 'AUR62004582' => 'cqu', 'AUR62010286' => 'cqu', 'AUR62023528' => 'cqu', 'AUR62031797' => 'cqu', 'AUR62033038' => 'cqu', 'AUR62039103' => 'cqu', 'BcaB03g11845' => 'bca', 'BcaB03g15655' => 'bca', 'BcaB04g19042' => 'bca', 'BcaC01g00918' => 'bca', 'BcaC01g03628' => 'bca', 'BcaC07g38891' => 'bca', 'BcaC07g38892' => 'bca', 'BcaC07g38893' => 'bca', 'BcaC08g45721' => 'bca', 'BcaNung03802' => 'bca', 'BcaNung05138' => 'bca', 'BolC1t00446H' => 'bol', 'BolC3t17327H' => 'bol', 'BolC3t20883H' => 'bol', 'BolC6t38610H' => 'bol', 'BolC7t46469H' => 'bol', 'BolC8t49450H' => 'bol', 'BraA01t00413Z' => 'bra', 'BraA03t13277Z' => 'bra', 'BraA03t15350Z' => 'bra', 'BraA07t30668Z' => 'bra', 'BraA08t33663Z' => 'bra', 'BraA08t35007Z' => 'bra', 'C01p04630' => 'bna', 'C03p50350' => 'bna', 'C03p85920' => 'bna', 'C06p35060' => 'bna', 'C07p60280' => 'bna', 'C08p18160' => 'bna', 'CAN.G126.47' => 'can', 'CAN.G202.8' => 'can', 'CAN.G216.7' => 'can', 'CAN.G499.8' => 'can', 'CAN.G790.40' => 'can', 'CANSAT01G0313' => 'cansat', 'CANSAT25G0070' => 'cansat', 'CANSAT25G0440' => 'cansat', 'CANSAT25G0909' => 'cansat', 'CARHR018350' => 'chi', 'CARHR060470' => 'chi', 'CARHR065050' => 'chi', 'CARHR094900' => 'chi', 'CARHR105680' => 'chi', 'CARHR242600' => 'chi', 'Carub.0001s1747' => 'cru', 'Carub.0002s1900' => 'cru', 'Carub.0003s1928' => 'cru', 'Carub.0003s2916' => 'cru', 'Carub.0003s2917' => 'cru', 'Carub.0003s2919' => 'cru', 'Carub.0007s0618' => 'cru', 'Ca_11082_v3' => 'car', 'Ca_14160_v3' => 'car', 'Ca_20948_v3' => 'car', 'CBR_g3076' => 'cbr', 'CBR_g8610' => 'cbr', 'Cc02_g19200' => 'ccan', 'Cc03_g14410' => 'ccan', 'Cc04_g00470' => 'ccan', 'Cc10_g11160' => 'ccan', 'CDE01G0109' => 'cde', 'CDE02G0739' => 'cde', 'CDE02G1108' => 'cde', 'CDE02G1574' => 'cde', 'CDE02G2155' => 'cde', 'CDE04G0202' => 'cde', 'CDE05G3014' => 'cde', 'CDE06G2051' => 'cde', 'CDE07G1631' => 'cde', 'Cfa003445' => 'cfa', 'Cfa004571' => 'cfa', 'Cfa012993' => 'cfa', 'Cfa012995' => 'cfa', 'Cfa018052' => 'cfa', 'Cfa022312' => 'cfa', 'Cfa024585' => 'cfa', 'Cfa026488' => 'cfa', 'Ciclev10000651m.g' => 'ccl', 'Ciclev10020311m.g' => 'ccl', 'Ciclev10024174m.g' => 'ccl', 'Ciclev10025148m.g' => 'ccl', 'Ciclev10028055m.g' => 'ccl', 'CiPaw.01G209700' => 'cil', 'CiPaw.05G010900' => 'cil', 'CiPaw.06G169800' => 'cil', 'CiPaw.07G234300' => 'cil', 'ClCG05G010250' => 'cla', 'ClCG07G014180' => 'cla', 'ClCG09G010140' => 'cla', 'COL.COLO4_10111' => 'col', 'COL.COLO4_19948' => 'col', 'COL.COLO4_32602' => 'col', 'Cpa.g.sc106.86' => 'cpa', 'Cpa.g.sc177.21' => 'cpa', 'Cpa.g.sc21.148' => 'cpa', 'Cpa.g.sc375.5' => 'cpa', 'Cre01.g019100' => 'cre', 'Cre02.g087300' => 'cre', 'Cre07.g324550' => 'cre', 'Cre07.g344400' => 'cre', 'Cre07.g344550' => 'cre', 'Cre07.g344600' => 'cre', 'Cre16.g689700' => 'cre', 'CsaV3_3G018240' => 'csa', 'CsaV3_3G031190' => 'csa', 'CsaV3_3G031200' => 'csa', 'CsaV3_7G024600' => 'csa', 'CsaV3_UNG227820' => 'csa', 'CsaV3_UNG227830' => 'csa', 'CsaV3_UNG227840' => 'csa', 'CSS0000561' => 'camsi', 'CSS0005661' => 'camsi', 'CSS0006403' => 'camsi', 'CSS0016973' => 'camsi', 'CSS0017991' => 'camsi', 'CSS0019362' => 'camsi', 'CSS0026600' => 'camsi', 'CSS0031569' => 'camsi', 'CSS0039143' => 'camsi', 'CSS0047612' => 'camsi', 'DCAR_016676' => 'dca', 'DCAR_016677' => 'dca', 'DCAR_021994' => 'dca', 'DCAR_022628' => 'dca', 'Dinv15759' => 'din', 'Dinv20362' => 'din', 'Dinv35921' => 'din', 'Dinv37804' => 'din', 'Dinv41779' => 'din', 'Dinv42186' => 'din', 'Dinv42187' => 'din', 'Duzib052G0257' => 'dzi', 'Duzib116G0867' => 'dzi', 'Duzib132G0515' => 'dzi', 'Duzib150G0834' => 'dzi', 'Duzib170G0484' => 'dzi', 'Duzib248G1386' => 'dzi', 'ECA233G5758' => 'eca', 'ECA234G4297' => 'eca', 'ECA236G3829' => 'eca', 'EL10Ac1g00154' => 'bvu', 'EL10Ac8g19460' => 'bvu', 'EL10Ac9g22288' => 'bvu', 'Eucgr.C03233' => 'egr', 'Eucgr.D02002' => 'egr', 'Eucgr.E00620' => 'egr', 'Eucgr.F02299' => 'egr', 'Eucgr.F04000' => 'egr', 'Eucgr.F04070' => 'egr', 'Eucgr.G01359' => 'egr', 'Eucgr.G01365' => 'egr', 'Eucgr.G01368' => 'egr', 'Eucgr.H03220' => 'egr', 'Eucgr.H03229' => 'egr', 'Eucgr.H03230' => 'egr', 'Eucgr.J00710' => 'egr', 'Eucgr.L02314' => 'egr', 'FAN02G3865' => 'fan', 'FAN05G0461' => 'fan', 'FAN05G3973' => 'fan', 'FAN09G0129' => 'fan', 'FAN13G0428' => 'fan', 'FAN14G5594' => 'fan', 'FAN15G1761' => 'fan', 'FAN18G0918' => 'fan', 'FAN20G0901' => 'fan', 'FAN24G1310' => 'fan', 'FAN27G2181' => 'fan', 'FvH4_2g05310' => 'fve', 'FvH4_5g31330' => 'fve', 'FvH4_6g37460' => 'fve', 'Glyma.04G110700' => 'gma', 'Glyma.07G003400' => 'gma', 'Glyma.08G223300' => 'gma', 'Glyma.10G261400' => 'gma', 'Glyma.13G372200' => 'gma', 'Glyma.20G129400' => 'gma', 'Gohir.A04G119500' => 'ghi', 'Gohir.A05G082900' => 'ghi', 'Gohir.A06G021600' => 'ghi', 'Gohir.A12G022400' => 'ghi', 'Gohir.A13G043500' => 'ghi', 'Gohir.D04G161100' => 'ghi', 'Gohir.D05G085800' => 'ghi', 'Gohir.D06G019100' => 'ghi', 'Gohir.D12G022800' => 'ghi', 'Gohir.D13G042000' => 'ghi', 'Gorai.008G023300' => 'gra', 'Gorai.009G087500' => 'gra', 'Gorai.010G023200' => 'gra', 'Gorai.012G149100' => 'gra', 'Gorai.013G046900' => 'gra', 'GSVIVG01003165001' => 'vvi', 'GSVIVG01009428001' => 'vvi', 'GSVIVG01016122001' => 'vvi', 'GSVIVG01020833001' => 'vvi', 'GSVIVG01025950001' => 'vvi', 'HanXRQChr04g0094161' => 'han', 'HanXRQChr05g0134451' => 'han', 'HanXRQChr07g0189981' => 'han', 'HanXRQChr09g0262621' => 'han', 'HanXRQChr10g0301601' => 'han', 'HanXRQChr12g0382121' => 'han', 'HanXRQChr16g0510111' => 'han', 'Haze_10163' => 'cav', 'Haze_16160' => 'cav', 'Haze_21348' => 'cav', 'Haze_21354' => 'cav', 'Haze_26505' => 'cav', 'Hma1.2p1_0090F.1_g045600' => 'hma', 'Hma1.2p1_0158F.1_g069880' => 'hma', 'Hma1.2p1_0796F.1_g219150' => 'hma', 'Hma1.2p1_1104F.1_g257450' => 'hma', 'Hma1.2p1_1325F.1_g275740' => 'hma', 'Hma1.2p1_2621F.1_g325590' => 'hma', 'HPP92_003713' => 'vpl', 'HPP92_026139' => 'vpl', 'Hund00145' => 'sun', 'Hund06324' => 'sun', 'Hund16765' => 'sun', 'Hund22373' => 'sun', 'Lalb_Chr01g0011751' => 'lal', 'Lalb_Chr02g0145341' => 'lal', 'Lalb_Chr04g0264751' => 'lal', 'Lalb_Chr06g0165481' => 'lal', 'Lalb_Chr15g0080101' => 'lal', 'Lalb_Chr21g0308381' => 'lal', 'Lj3g0001770' => 'lja', 'Lj3g0006654' => 'lja', 'Lj3g0016198' => 'lja', 'Lj5A213T89' => 'lonja', 'Lj5C26G2' => 'lonja', 'Lj5g0021739' => 'lja', 'Lj7A623G47' => 'lonja', 'Lj9A321T83' => 'lonja', 'Lsat_1_v5_gn_1_39601' => 'lsa', 'Lsat_1_v5_gn_5_114741' => 'lsa', 'Lsat_1_v5_gn_5_67120' => 'lsa', 'Manes.02G199700' => 'mes', 'Manes.05G177600' => 'mes', 'Manes.07G069600' => 'mes', 'Manes.10G074000' => 'mes', 'Manes.16G045550' => 'mes', 'Mapoly0015s0127' => 'mpo', 'Mapoly0030s0029' => 'mpo', 'MBI14_g37769_MAGBIO' => 'mbi', 'MBI16_g00682_MAGBIO' => 'mbi', 'MBI18_g05084_MAGBIO' => 'mbi', 'MCO01G185' => 'mco', 'MCO02G374' => 'mco', 'MCO05G063' => 'mco', 'MCO11G798' => 'mco', 'MCO12G354' => 'mco', 'MD05G1088400' => 'mdo', 'MD08G1217300' => 'mdo', 'MD09G1157900' => 'mdo', 'MD17G1143900' => 'mdo', 'Medtr1781s0020' => 'mtr', 'Medtr1g107480' => 'mtr', 'Medtr3g005970' => 'mtr', 'Medtr4g005880' => 'mtr', 'MELO3C019542.2' => 'cme', 'MELO3C024090.2' => 'cme', 'MELO3C025791.2' => 'cme', 'Migut.B00383' => 'egut', 'Migut.D00899' => 'egut', 'Migut.I01151' => 'egut', 'Migut.N03357' => 'egut', 'MSTRG.10897' => 'ama', 'MSTRG.20182' => 'ama', 'MSTRG.21622' => 'ama', 'MSTRG.22461' => 'ama', 'MSTRG.22509' => 'ama', 'MSTRG.27742' => 'ama', 'MSTRG.4530' => 'ama', 'MSTRG.4531' => 'ama', 'MSTRG.5345' => 'ama', 'MSTRG.9551' => 'ama', 'Nitab4.5_0000167g0200' => 'nta', 'Nitab4.5_0001185g0080' => 'nta', 'Nitab4.5_0001539g0010' => 'nta', 'Nitab4.5_0001579g0040' => 'nta', 'Nitab4.5_0001596g0020' => 'nta', 'Nitab4.5_0001691g0050' => 'nta', 'Nitab4.5_0002543g0160' => 'nta', 'Nitab4.5_0002885g0060' => 'nta', 'Nn1g04712' => 'nnu', 'Nn1g09668' => 'nnu', 'Nn2g12300' => 'nnu', 'Nn3g19430' => 'nnu', 'Nn5g27453' => 'nnu', 'Nn5g30410' => 'nnu', 'Nn8g40392' => 'nnu', 'Oeu014973.1' => 'oeu', 'Oeu029228.1' => 'oeu', 'Oeu039449.1' => 'oeu', 'Oeu044289.1' => 'oeu', 'Oeu049650.1' => 'oeu', 'Oeu063233.1' => 'oeu', 'Os04g0650800' => 'osa', 'Os06g0655100' => 'osa', 'Os07g0263400' => 'osa', 'Os07g0264100' => 'osa', 'Os08g0447000' => 'osa', 'Peaxi162Scf00003g02445' => 'pax', 'Peaxi162Scf00038g02432' => 'pax', 'Peaxi162Scf00152g00234' => 'pax', 'Peaxi162Scf00152g00242' => 'pax', 'Peaxi162Scf01013g00230' => 'pax', 'Peaxi162Scf01013g00239' => 'pax', 'PGR042G0570' => 'pgr', 'PGR042G3831' => 'pgr', 'PGR083G1668' => 'pgr', 'PGR102G1898' => 'pgr', 'PGSC0003DMG400009159' => 'stu', 'PGSC0003DMG400018130' => 'stu', 'PGSC0003DMG400023264' => 'stu', 'PGSC0003DMG400027624' => 'stu', 'PGSC0003DMG400035491' => 'stu', 'Phvul.005G002200' => 'pvu', 'Phvul.007G040600' => 'pvu', 'Phvul.008G256300' => 'pvu', 'Potri.001G300900' => 'ptr', 'Potri.002G122700' => 'ptr', 'Potri.008G009500' => 'ptr', 'Potri.009G096600' => 'ptr', 'Potri.010G249600' => 'ptr', 'Potri.013G104200' => 'ptr', 'Potri.014G022800' => 'ptr', 'Pp3c11_15420' => 'ppa', 'Pp3c16_19100' => 'ppa', 'Pp3c1_7910' => 'ppa', 'Pp3c5_20110' => 'ppa', 'Pp3c7_10960' => 'ppa', 'Pp3c7_18950' => 'ppa', 'Pp3c7_19020' => 'ppa', 'PRCOL_00001767' => 'pco', 'PRCOL_00002795' => 'pco', 'PRCOL_00002814' => 'pco', 'PRCOL_00002871' => 'pco', 'PRCOL_00004197' => 'pco', 'Prupe.1G556800' => 'ppe', 'Prupe.3G168100' => 'ppe', 'Prupe.8G134300' => 'ppe', 'Psat5g232400' => 'psa', 'Psat6g219520' => 'psa', 'Psat7g263880' => 'psa', 'PSO017G2270' => 'pso', 'PSO063G5107' => 'pso', 'PSO170G0801' => 'pso', 'PSO170G4690' => 'pso', 'PSO210G7083' => 'pso', 'PSO782G0164' => 'pso', 'QL02p003847' => 'qlo', 'QL02p023588' => 'qlo', 'QL05p083397' => 'qlo', 'QL11p033963' => 'qlo', 'QL11p033997' => 'qlo', 'QL11p034038' => 'qlo', 'RcHm_v2.0_Chr2g0150301' => 'rch', 'RcHm_v2.0_Chr6g0255451' => 'rch', 'RcHm_v2.0_Chr7g0226521' => 'rch', 'RcHm_v2.0_Chr7g0226551' => 'rch', 'Rhsim02G0204900' => 'rsi', 'Rhsim05G0088500' => 'rsi', 'Rhsim06G0055300' => 'rsi', 'Rhsim12G0214000' => 'rsi', 'Sabra02G0096100' => 'sbr', 'Sabra08G0005500' => 'sbr', 'Sabra09G0074200' => 'sbr', 'Sabra10G0194200' => 'sbr', 'Sabra13G0090100' => 'sbr', 'Sabra14G0015700' => 'sbr', 'Sabra16G0189000' => 'sbr', 'SalBow6G1159' => 'sbo', 'SalBow6G2141' => 'sbo', 'SalBow7G3804' => 'sbo', 'Sc01g0002050' => 'sci', 'Sc08g0001440' => 'sci', 'Sc10g0008530' => 'sci', 'Sed0000608' => 'sed', 'Sed0002208' => 'sed', 'Sed0009064' => 'sed', 'Sed0016515' => 'sed', 'SEGI_12091' => 'sgi', 'SEGI_18069' => 'sgi', 'SEGI_25928' => 'sgi', 'SGA_v2.0_scaffold225G43076' => 'sas', 'SGA_v2.0_scaffold32G13037' => 'sas', 'SGA_v2.0_scaffold56G20007' => 'sas', 'SGA_v2.0_scaffold68G22813' => 'sas', 'SMO134G0082' => 'smo', 'SMO137G0006' => 'smo', 'SMO137G0330' => 'smo', 'SMO143G0071' => 'smo', 'SMO361G0036' => 'smo', 'SMO361G0603' => 'smo', 'Solyc03g112070.4' => 'sly', 'Solyc03g123830.4' => 'sly', 'Solyc10g049890.3' => 'sly', 'Solyc11g020060.2' => 'sly', 'Sopen03g031170' => 'spe', 'Sopen03g041580' => 'spe', 'Sopen06g023790' => 'spe', 'Sopen10g019950' => 'spe', 'Sopen11g010190' => 'spe', 'Sp1g15820' => 'spa', 'Sp3g17530' => 'spa', 'Sp3g28600' => 'spa', 'Sp5g27280' => 'spa', 'Sp7g31970' => 'spa', 'TAR077G0001' => 'tar', 'TAR376G0255' => 'tar', 'TAR376G0611' => 'tar', 'TAR625G1204' => 'tar', 'TAR628G1015' => 'tar', 'TAR628G1272' => 'tar', 'TAR629G3228' => 'tar', 'THA.LOC104804388' => 'tha', 'THA.LOC104807246' => 'tha', 'THA.LOC104810629' => 'tha', 'THA.LOC104814757' => 'tha', 'THA.LOC104819558' => 'tha', 'THA.LOC104825375' => 'tha', 'Thecc.02G107100' => 'tca', 'Thecc.06G016500' => 'tca', 'Thecc.08G000500' => 'tca', 'Thecc.09G289100' => 'tca', 'Thecc.09G289200' => 'tca', 'Thhalv10000359m.g' => 'esa', 'Thhalv10007072m.g' => 'esa', 'Thhalv10018793m.g' => 'esa', 'Thhalv10020363m.g' => 'esa', 'Thhalv10022606m.g' => 'esa', 'Thhalv10024715m.g' => 'esa', 'TPR.G13871' => 'tpr', 'TPR.G25511' => 'tpr', 'TPR.G38707' => 'tpr', 'TWI18G0849' => 'twi', 'TWI31G0359' => 'twi', 'TWI56G0999' => 'twi', 'TWI59G0211' => 'twi', 'TWI79G0960' => 'twi', 'unitig_21.g20247' => 'ugi', 'unitig_21.g20735' => 'ugi', 'unitig_748.g7479' => 'ugi', 'unitig_94.g28310' => 'ugi', 'vmacro11201' => 'vma', 'vmacro11202' => 'vma', 'vmacro17064' => 'vma', 'vmacro19522' => 'vma', 'vmacro19523' => 'vma', 'vmacro21484' => 'vma', 'vmacro23439' => 'vma', 'vmacro23440' => 'vma', 'VMungo0647G0091' => 'vmu', 'VMungo0720G2743' => 'vmu', 'VMungo1080G0499' => 'vmu', 'Zm00001eb040890' => 'zma', 'Zm00001eb068270' => 'zma', 'Zm00001eb097200' => 'zma', 'Zm00001eb389520' => 'zma', 'Zm00001eb432330' => 'zma' ) $gf_id = 'HOM05D001181' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001181' ) $data_identifier = 'HOM05D001181' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 7, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 7, 'csa' => (int) 7, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 14, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 10, 'nta' => (int) 8, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 7, 'pco' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 6, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 8, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432330' $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